Thanks for posting and trying InVEST! Did you calibrate the half saturation constant input at all? It’s a bit hidden in the User’s Guide but suggests:
This is the value of the parameter k in equation (4). By default it is set to 0.5 but can be set equal to any positive floating point number. In general, you want to set k to half of the highest grid cell degradation value on the landscape. To perform this model calibration you will have to the run the model once to find the highest degradation value and set k for your landscape. For example, if a preliminary run of the model generates a degradation map where the highest grid-cell degradation level is 1 then setting k at 0.5 will produce habitat quality maps with the greatest variation on the 0 to 1 scale (this helps with visual representation of heterogeneity in quality across the landscape).
Can you try this and let us know if you see a better range of values that are closer to what you’d expect?